Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014189.1 Corchorus capsularis cultivar CVL-1 contig14210, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 28437
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:768 original size:33 final size:33
Alignment explanation
Indices: 731--838 Score: 146
Period size: 33 Copynumber: 3.3 Consensus size: 33
721 GCGCCTAGCG
* *
731 ATGGCCGGTTG-TGGCCGGACATGTCCATGTCGC
1 ATGGCCGG-TGATGGCCGGACATCTCCAAGTCGC
*
764 ATGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
1 ATGGCCGGTGATGGCCGGACATCTCCAAGTCGC
* * *
797 GTGGCCGGTGTTGGCCGGACTTCTCCAAGTCGC
1 ATGGCCGGTGATGGCCGGACATCTCCAAGTCGC
830 ATGGCCGGT
1 ATGGCCGGT
839 CAGTAGTGCT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
32 2 0.03
33 64 0.97
ACGTcount: A:0.12, C:0.29, G:0.37, T:0.22
Consensus pattern (33 bp):
ATGGCCGGTGATGGCCGGACATCTCCAAGTCGC
Found at i:7729 original size:21 final size:21
Alignment explanation
Indices: 7703--7760 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
7693 TTACAATTTT
*
7703 AGAAGCCAAATTGTCTTTCAA
1 AGAAGCCAAAATGTCTTTCAA
*
7724 AGAAGCCAAACTGTCTTTCAA
1 AGAAGCCAAAATGTCTTTCAA
7745 AGAAGCCAAAATGTCT
1 AGAAGCCAAAATGTCT
7761 AATAAGCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (21 bp):
AGAAGCCAAAATGTCTTTCAA
Found at i:16810 original size:38 final size:38
Alignment explanation
Indices: 16759--16835 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
16749 GATCCCCTTT
16759 ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
1 ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
*
16797 ACATTTAATGCTAATCTTCTTTACTTGCAAGCAAAGTA
1 ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
16835 A
1 A
16836 AATCTAACGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (38 bp):
ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
Found at i:21135 original size:118 final size:118
Alignment explanation
Indices: 20922--21159 Score: 458
Period size: 118 Copynumber: 2.0 Consensus size: 118
20912 AATTACACCA
20922 GGTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAATCCAACTCCTTAGACA
1 GGTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAATCCAACTCCTTAGACA
*
20987 GAATTTGCCTAGACATGTAATTAAAGCACAATGACAACCTCTAGTGTCAAATG
66 GAATTTGCCTAGACATGTAATTAAAACACAATGACAACCTCTAGTGTCAAATG
21040 GGTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAATCCAACTCCTTAGACA
1 GGTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAATCCAACTCCTTAGACA
*
21105 GAATTTGCCTAGACATGTAATTAAAACACAATGACAACTTCTAGTGTCAAATG
66 GAATTTGCCTAGACATGTAATTAAAACACAATGACAACCTCTAGTGTCAAATG
21158 GG
1 GG
21160 AATTACTTAT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (118 bp):
GGTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAATCCAACTCCTTAGACA
GAATTTGCCTAGACATGTAATTAAAACACAATGACAACCTCTAGTGTCAAATG
Found at i:21275 original size:30 final size:30
Alignment explanation
Indices: 21213--21611 Score: 638
Period size: 30 Copynumber: 13.2 Consensus size: 30
21203 CATGGTGCAT
*
21213 ATGACAACTTCTGGTGTCAATTGAATAAAATC
1 ATGACAACTTCTGGTGTCAATTG--CAAAATC
*
21245 ATGACAACTTTTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
21275 ATGACAACTTATGGTGTCAATTGCAAAAATC
1 ATGACAACTTCTGGTGTCAATTGC-AAAATC
*
21306 ATGACAACTTTTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
21336 ATGACAACTTATGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
21366 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
21396 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
21426 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
21456 ATGACAACTTCTGGTGTCAATT-CAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
21485 ATGACAACTTTTGGTGTCATTTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
21515 ATGACAACTTCTGGTGTCATTTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
21545 ATGACAACTTCTGGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
**
21575 ATGACAACTTCTAATGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
21605 ATGACAA
1 ATGACAA
21612 ATGTGTCATT
Statistics
Matches: 351, Mismatches: 14, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
29 26 0.07
30 274 0.78
31 29 0.08
32 22 0.06
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:21548 original size:149 final size:150
Alignment explanation
Indices: 21213--21611 Score: 647
Period size: 149 Copynumber: 2.6 Consensus size: 150
21203 CATGGTGCAT
* *
21213 ATGACAACTTCTGGTGTCAATTGAATAAAATCATGACAACTTTTGGTGTCAATTGCAAAATCATG
1 ATGACAACTTCTGGTGTCAATTG--CAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATG
* *
21278 ACAACTTATGGTGTCAATTGCAAAAATCATGACAACTTTTGGTGTCAATTGCAAAATCATGACAA
64 ACAACTTCTGGTGTCAATTGC-AAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAA
21343 CTTATGGTGTCAATTGCAAAATC
128 CTTATGGTGTCAATTGCAAAATC
21366 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
*
21431 AACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATT-CAAGATCATGACAACTT
66 AACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTT
* * *
21495 TTGGTGTCATTTGCAAGATC
131 ATGGTGTCAATTGCAAAATC
* * *
21515 ATGACAACTTCTGGTGTCATTTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGATCATGAC
1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
**
21580 AACTTCTAATGTCAATTGCAAAATCATGACAA
66 AACTTCTGGTGTCAATTGCAAAATCATGACAA
21612 ATGTGTCATT
Statistics
Matches: 233, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
149 125 0.54
150 27 0.12
151 58 0.25
153 23 0.10
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (150 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
AACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTT
ATGGTGTCAATTGCAAAATC
Found at i:22585 original size:38 final size:38
Alignment explanation
Indices: 22534--22608 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
22524 TCCCCTTTAC
22534 ATTTAATACTAATCTGCTTTACTTGCAAGCAAAGTAAT
1 ATTTAATACTAATCTGCTTTACTTGCAAGCAAAGTAAT
* *
22572 ATTTAATGCTAATCTTCTTTACTTGCAAGCAAAGTAA
1 ATTTAATACTAATCTGCTTTACTTGCAAGCAAAGTAA
22609 AATCTAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (38 bp):
ATTTAATACTAATCTGCTTTACTTGCAAGCAAAGTAAT
Found at i:22997 original size:15 final size:16
Alignment explanation
Indices: 22971--23000 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22961 GGTTTTTGCT
22971 TCCTACTTCCTTTCCA
1 TCCTACTTCCTTTCCA
22987 TCCTA-TTCCTTTCC
1 TCCTACTTCCTTTCC
23001 TCCCTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (16 bp):
TCCTACTTCCTTTCCA
Found at i:24103 original size:2 final size:2
Alignment explanation
Indices: 24096--24125 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24086 AAATAAGAAA
24096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24126 GGAAAATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.